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OBJECTIVE The aim of this study was to construct a gene co-expression network to identify key modules and genes in people with generalized aggressive periodontitis. METHODS We used database GSE79705 to construct a co-expression network by weighted gene co-expression network analysis (WGCNA). In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were conducted. RESULTS A total of 51 co-expression modules were conducted, darkseagreen1 and blue1 modules were the most significantly related to generalized aggressive periodontitis. Genes in the darkseagreen1 module enriched in affecting cellular response to tumor necrosis factor and vascular endothelial growth factor production, and the blue1 module enriched in the regulation of ion transport, proteinaceous extracellular matrix and neuropeptide binding. Besides, we found that 4 hub genes (SNRPG, MRPL22, MRPS18C and CEP290) played an important role in the occurrence of generalized aggressive periodontitis. CONCLUSION Through this study, we identified two modules and four hub genes associated with generalized aggressive periodontitis. Besides, 4 hub genes (SNRPG, MRPL22, MRPS18C and CEP290) can be expected to trigger new therapeutic drug development for generalized aggressive periodontitis.